Pokemon Mystery Dungeon Hero x Partner One-Shots
by MarioandLuigiThePaperJamBros
Summary: All the games in the Pokemon Mystery Dungeon series are all different in someway shape of form, but one thing remains consistent, which is the shipping between two Pokemon, more specifically Hero x Partner. From Red/Blue Rescue Team to Super Mystery Dungeon, here is a collection of One-Shots from each of the games. My change cover if I decide to do others besides Hero x Partner.


**Justin: Hey guys! It's the man you know and the guy that loves to throw as Mario! Welcome back to another story!**

 **So yeah... I want to apologize. I've been absent for 6 months with no story update, but I am not dead. I had a really busy school year and and I grew as an artist now. But I didn't abandon at all.**

 **As you probably already now, I have gotten into Pokemon Mystery Dungeon and I actually boarded the Hero x Partner Train, but that should come as no surprise... but then I thought... Let's make Shipping Stories out of cute parts of each game in the series and thus this series has been born.**

 **Pikachu: Come on you return and you don't even update our-**

 **Justin: No.**

 **Pikachu: *Frowns* Aw...**

 **Justin: Anyway, yeah, I may be a bit rusty returning to Fanfiction, but I think I did good. I also want to wish everyone a Merry Christmas and Happy New Year!**

 **So for this first chapter, I took one of the saddest parts of Pokemon Mystery Dungeon Red/Blue Rescue Team. If you thought you couldn't cry anymore when you saw this cutscene, just a warning I tried to make it even more sad. Also I added one part that fans of another series should be familiar with.**

 **Welp that's everything! Now disclaimer!**

 **I do not own any characters, the general plot, or any music in this story or series. They all belong to their respective copyrights.**

* * *

 **Song List in Order of When They Appear**

 **1)** **"Grima has returned to slumber" - Fire Emblem Awakening** **OR** **Aftermath (Original or Remastered) - Pokemon Mystery Dungeon**

 **2)** **Premonition (Receive or Approval) - Fire Emblem Fates OR Farewell (Original or Remastered)**

 **3)** **Staff Credits - Super Mario Galaxy 1 or 2**

* * *

 **Chapter 1**

 **Bonds Across Space and Time**

 **Cyndaquil x Chikorita**

'...The last thing I remember was that... my partner Chikorita and I... was fought Raquayza and won... we then saw the shooting star coming down towards us... Rayqauza warned us about what would happen if Hyper Beam fails... The last thing we said was...' An ex-human Cyndaquil thought

 _"So?! We accepted that from the start!" Chikorita exclaimed._

 _"We are willing to accept what fate may be!" Cyndaquil followed up._

 _The legendary looked at the two young un-evolved Pokemon and nodded. "Well said!" It's mouth began to glow and started to store energy into a beam like energy source. It looked to the sky on the course of the falling star as it gave one last message to the pair. "Seize your own destiny!" Rayquaza fired it's massive beam straight up at the shooting star..._

 _"It's close Cyndaquil!" Chikorita panicked._

 _"Stay close!" Cyndquil yelled back. Cyndquil and Chikorita then hugged each other as closed their eyes shut as the Fire Mouse said, "I won't let you go... I promise!"_

'Everything went blank after that... the star swallowed all of us up...I felt my Leaf Pokemon partner beside me...collapsed just as I was... I do not know where Chikorita and I were... this is not a dream... all I know is that I am now adrift... as a spirit... what... what is going to happen now...?' The Cyndaquil thought to himself as he faintly saw a familiar shaped shadow approach him. '...Gengar...?' He was then dragged by him along what was seemed like space... empty space... 'Gengar said that he was going to take Chikorita and I to the Dark World... is this how it ends... being abandoned in a world we don't know...? Will we ever see everyone again...?' Everything suddenly went black for the Cyndaquil.

"...Hey." A voice said.

"...Hey, can you hear..." The voice said again.

'Hm...?' The Cyndaquil thought.

'I-I hear... voices...' Thought the Chikorita.

They both used their strength to open their eyes a bit to see the silhouette of Alakazam. "Snap out of it!" He then yelled.

The Cyndaquil then weakly questioned, "H-huh...? Why... are we back here...?"

Chikorita struggled a bit, but she managed to stand. "...Ack... Cynda...quil...w-we're... alive?"

All the Pokemon that were around them gave a sigh of relief as Alakazam said, "Hah... Looks like you've regained consciousness!"

Cyndaquil managed to stand up as well, but not without a bit of struggling much like Chikorita had. He looked around and then faced his partner. "Y-yeah... we're alive. Gengar must have saved us back there... I'm sure of it."

"Yeah, he must have." Chikorita replied with a nod.

The group gave smiles and cheers of joy and relief with Lombre being the first to speak. "Awesome! You both are alive haha!" He exclaimed with a cheer. "You know, you two really had us all panicking for a second there."

Cyndaquil and Chikorita smiled awkwardly and sweat-dropped, saying in unison, "Sorry about that."

"You two were incredible! What you did was absolutely amazing!" Octiliary chimed in with glee.

Caterpie sniffed, "I-I'm glad so glad you two are safe, it's fantastic!" he said with tears of joy in his eyes.

Cyndaquil and Chikorita looked at everyone with a smile as Cyndaquil nodded as he gave a warm smile to everyone, and Chikorita said, "Everyone...thank you..." with a twinkle in her eye. She then had a questioned-surprised look, "Oh! But, what about the star?! Is everything okay, what happened to it?!"

"KWAAAAAAAAAAAAAAAAHHHHHHHH!"

Everyone turned to the mystic sight seer bird, Xatu. "Fear not! The star has been destroyed, it is no more. Overtime, the disasters of this world will calm and soon come to an end." he explained. Everyone had looks of happy surprise.

Chikorita turned to Cyndaquil with a large twinkle in her lush eyelash eyes, "W-we did it Cyndaquil!"

Cyndaquil nodded and replied, "The star has been destroyed, and the balance has been restored to the world."

Chikorita nodded happily and followed up, "Everything worked! We've actually won peace for the world and everybody else!"

 ***Song:** **"Grima has returned to slumber" - Fire Emblem Awakening** **OR** **Aftermath (Original or Remastered) - Pokemon Mystery Dungeon***

The crowd of Pokemon around them cheered as loud as they could giving hugs to each other and laughing with joy!

Snubbull started, "This is the best!"

Charizard of team ACT started, "This joyous victory and occasion calls for a celebration!"

Blastoise readied his cannon in excitement, "I'll kick this off by shooting my Hydro Pump" The trajectory just happened land Lombre in the line of fire.

Lombre ducked in a bit of nervousness, "Whoa! Hold on! Don't point that at me and don't think about shooting this way!"

Shiftry however, contradicted him, "No no! Let it loose, we wanna see the firing! Haha!"

The Jolly Pokemon didn't look too jolly at that moment, "You've gotta be kidding me! I'm getting outta here!" He proceeded to leave until Octillary grabbed him with his tentacles.

"Where you going? Don't leave, in fact I'll secure you so you can't escape." Octillary said with a smirk.

Lombre had a surprised look, "Wh-wha?"

Charizard laughed, "Oh? Not bad!"

Everyone but Cyndaquil approached Lombre and surrounded him. "Wait you're serious?! Nonononono! Please don't!"

Chikorita said, "Looks like you're in a real pickle now Lombre, hehe." Everyone laughed.

The Fire Mouse Pokemon looked at everyone and gave a chuckle, "Looks like everyone can now rest easy." His smile turned into a bit of a sad look though, "But... now that everything is back to normal in the Pokemon World... the world is saved... and that means..."

 ***Song Stop***

"Cyndaquil..." A voice from nowhere spoke to him. He looked around and saw a elegant Pokemon in what looks like a white dress materialize before him.

"...Gardevoir..." the ex-human Cyndaquil spoke.

 ***Song: Premonition (Receive or Approval) - Fire Emblem Fates OR Farewell (Original or Remastered)**

Gardevoir nodded and said, "We owe everything to you, Cyndaquil, and Chikorita as well as your friends. Peace has returned to our world thanks to you and all of your allies' valiant efforts. Thank you for everything."

Cyndaquil nodded but had a sad look on his face. "But... I guess... that means... it's that time... right...?"

The Psychic Type's face formed into a sorrowful and apologetic look, but nodded, "Yes. Your role here as a Pokemon has ended. You will soon return to the human world, your own world. It's... time to bid everyone farewell."

Cyndaquil looked down and to everyone who was still celebrating. "Farewell... to everyone... to Chikorita..."

Gardevoir almost had a tear in her eye as he mentioned Chikorita's name. "Chikorita... she means a lot to you doesn't she?"

Cyndaquil nodded, "I made her a promise... that I would stay with her forever... to be her best friend until the end of time..."

Gardevoir gave a really apologetic look as she simply replied, "Oh..."

 **Flashback**

 _Cyndaquil and Chikorita had just returned from being fugitives and decided to rest up in the team base._

 _Cyndaquil sighed, "Man... I never though being fugitives would be tiring._

 _The Leaf Pokemon replied, "I know right? It was scary at some points, but I guess it was a bit of fun."_

 _Her partner and leader of the team nodded, "But hey, we made it through the adventure together and we came out ever stronger from it, so yeah I guess it wasn't as bad as we thought it was going to be."_

 _Chikorita chuckled, "Yeah, imagine if Team A.C.T was to fight us before we left, boy wouldn't that have been the fight of our life."_

 _Both of them gave out a bit of a laugh for awhile until Chikorita had to leave before it got dark. At the front entrance though, she turned around._

 _"Hey Cyndaquil?" Chikorita asked._

 _"Hm?" Cyndaquil replied tilting his head._

 _The Fire Type's partner shuffled her feet trying to find the words to say. "U-um..."_

 _"Do you need to tell me something?" Cyndaquil curiously asked._

 _Chikorita spoke, "I-I know I've been asking you to make me promises... but... um."  
_

 _However, the Cyndaquil smiled and caught on very quickly, "You're asking me to make another one to you yes?"_

 _Chikorita chuckled a bit, "Y-yeah."_

 _Cyndaquil nodded, "Sure, what is it?"_

 _Chikorita looked at him, "Will you promise me that we will stay together forever? I want to be your best friend."_

 _Cyndaquil blushed slightly at that. "What? What brought this up?"_

 _Chikorita looked down and shuffled her tiny stubs again turning red slightly as well, "It's that, we've been partners and friends for sometime now and it's just... I didn't have any friends before I met you. After we came here you said that we can become friends and that made you my first ever true friend. With you, we made even more friends, but I know this would have never been possible if I never met you Cyndaquil. That's why I want our friendship to last."_

 _Cyndaquil was at a loss of words, only saying, "W-wow."_

 _Chikorita looked back at him, "So... will you promise me Cyndaquil, that we will be with each other, you will never leave me behind?"_

 _Cyndaquil thought for a bit then smiled. "Of course, I will. I'll never leave you."_

 _In that moment his partner's eye's glimmered and she hugged him. "Thank you Cyndaquil, thank you so much!" It shocked him a bit and he blushed redder but he returned the hug nonetheless with a smile._

 _"Anytime Chikorita, anytime." They continued to hug it out._

 _Cyndaquil replied in the hug turning redder as well. "Thank you Cyndaquil."_

 **Flashback End**

"And now... I can't even keep that promise to her..." Cyndaquil finished sadly. He then saw glowing beneath his feet and saw that it was coming from him and he knew what it meant. "It's finally come... This time has finally arrived... Time for me to go back to my own world... away from Chikorita... and everyone else..."

Gardevoir although sad to say it, spoke up, "Cyndaquil... I'm very sorry for this... To everyone... I really am..."

Cyndaquil simply nodded in understanding, "I understand... I will accept my fate to return."

Gardevoir nodded back, "Please bid everyone farewell..." Cyndaquil nodded and she said. "Farewell... Cyndaquil." And with that she faded away into the air.

The Fire Type simply looked straight ahead at everyone. Caterpie was the first to notice. "Huh? Cyndaquil?" This caused everyone to turn towards him.

Chikorita was shocked to see her partner's body glowing, "Ah! Cyndaquil! Your body is... What's happening to you?"

Cyndaquil simply said, "At...last... This world... is safe... We've... achieved peace... for this... world..." He then suddenly collapsed to the floor as being turned back into a human by the last is causing his body as a Pokemon to give out.

Everyone gave shocked looks and Chikorita yelled his name as she ran over to him. "Cyndaquil!"

The Grass Type ran over to his side, "Cyndaquil! Are you okay?! You don't look good! Why is your body glowing?!"

Cyndaquil weakly lifted his head to meet her eyes, "Ughhh... I'm sorry Chikorita. I promised you that I wouldn't leave your side. But... I'm not sure...I don't think... I can keep my word...

Chikorita was stunned, "W-wha...?"

Cyndaquil looked to everyone behind her. "I'm sorry everyone... my time here... is at an end... I have to leave..." This caused everyone to gasp.

"What?!" Snubbull exclaimed.

"Wh-what are you saying?!" Bellsprout followed up.

"Wh-what do you mean Cyndaquil? I don't understand! What do you mean leave." Chikorita yelled.

Cyndaquil started to explain, "My role here... has... ugh... come to... an end... I have to... return to... the human world... my own world..."

Alakazam shouted, "Unbelievable!"

Tyranitar followed up, surprised, "Go back... to the human world?!

Chikorita shouted in horror, "H-huh?! W-why? Why?! I-I don't understand! Why do you... have to leave?!" She then started to look very sad and sorrow, "Didn't we... aren't we best friends like you said...?"

Cyndaquil looked sad and regretful but explained, "Yes we are. I made the promise that we'd be... best friends forever... I wish... it didn't have to be this way... But I was turned into a Pokemon... to save you and everyone else in this world... After that Gardevoir told me... that I would then have to leave... whether I wanted to or not..."

Chikorita asked, "B-but if you knew about this... wh-why... why didn't you tell me?! If you knew that this was coming... that you would have to leave after the star is destroyed... why didn't you... tell me... why...?"

Cyndaquil replied, "Because... I made a promise to you... I... didn't want to make you sad... That was the last thing I want...But... I'm sorry that I never said anything... and now you're seeing it happening now..."

Chikorita started to tear up but held them back, "Please! You can't just leave like this! We just did it Cyndaquil, we saved the world, we won peace!"

Cyndaquil just nodded.

"B-but what is it worth, if you never get to experience it for yourself? What is it worth...?" Chikorita continued.

Cyndaquil just smiled, "It is worth it Chikorita. I now know you and everyone else will be safe... That is worth everything to me."

Chikorita's tears started to come out as she sobbed. "C-C-Cydnaquil..."

"Will you listen to one more selfish request of mine?" Cyndaquil asked his partner.

Chikorita sniffled and replied. "W-what is it?"

Cyndaquil smiled and tried to keep a happy look as he said, "I want you and everyone else to live a happy and joyous life. Don't let my disappearance sour your victory."

Chikorita did not reply, just sobbing as she looked as the lights emitting from her partner is starting to get brighter and stronger.

"The world's disasters has been alleviated...a world at peace... the world that we and everyone else have always dreamed of... That's the type of world I sacrificed myself for and it was all worth it in the end." Cyndaquil expressed. The lights from him gave a quick burst as he felt and everyone else saw.

"Th-the light!" Chikorita said weakly surprised.

"It looks like my time is almost up... Chikorita..." Cyndaquil said.

Chikorita's tears continued to drop onto the ground, "D-don't go Cyndaquil... I... What am I going to do... when you're gone?"

Cyndaquil reassured, "You'll be alright."

Everyone gave very sad and some tearful looks towards the Chikorita and Cyndaquil. The ex-human knew his time was running as the light began to consume his body and everyone and Chikorita looked shocked and horrified.

Cyndaquil looking at Chikorita's face made him realize why he trusted her above all else. He knew what he felt for her, and to leave so suddenly broke his heart... but he gave her one last message. "I'm never going to forget you... and I made and kept many promises to you through our whole adventure to show how much... our friendship means to me. So now, it's your turn to make me a promise Chikorita..." He laid his head down for brief moment.

The Grass Type had a pained expression as she knew what he meant. "Cyndaquil... no..."

Chikorita saw various parts of Cyndaquil's body be slowly consumed by the light as Cyndaquil was starting to give out as he made staggered yet pained breathing. Cyndaquil lifted his head up and he with a weak smile, weakly spoke to her his last words. "Can I see you smile for me one last time?" His eyes started to water and a tears streamed down his face, but avoided making a sad look. "One more smile... before I go." He then reached his paw out toward Chikorita. "That's right... Lovely..." His last few tears streamed down his face before the light finally consumed the rest of his body and he disappeared completely in one burst of light as the the large parts floated up to the sky and tiny light bursts floated down over everyone.

"NO!" Chikorita yelled. "No... please! WAAUUUGGHHH!" She clutched her head with both her front paws as her head was on the ground. "Not you Cyndaquil! Please not you, I need you Cyndaquil! I CAN'T LOSE YOU NOW!" She sobbed loudly for a bit as a bunch of her tears fell to the floor. However, she remembered knew crying was not what Cyndaquil wanted for his last wish so, she sniffled a bit and stopped. "...I will keep my promise, Cyndaquil." She removed her hands from her head and she stood up. "I won't let your sacrifice be in vain."

Everyone else gave tearful looks to them, but saw Chikorita stand and stopped crying, but still had tears running down their faces, but then Chikorita spoke up.

"Everyone... we have a lot of work ahead of us. Let's make this world a place we can be proud of again. Everyone, starting tomorrow, let's give it our all so the world and everyone in it can remain peaceful. Let's honor Cyndaquil's last wish."

Everyone wiped their tears from their eyes and nodded while saying, "Right!"

Chikorita then smiled a bit as she looked up at the sky, "Cyndaquil... You saved all of us knowing that you may never see us again... But despite all that... I hope we will meet again someday, somehow..."

Chikorita and everyone else started to walk back home to Cyndaquil and Chikroita's team base.

 **Scene Shift  
*Song: Rosalina's Storybook - Super Mario Galaxy***

The light that Cyndaquil is continued to rise up into the air and into the night sky where the stars became visible. Cyndaquil from inside awoke, "Hmm...? What is this...? I'm rising up into the sky... Is this this my spirit...? Am I... returning to my world...? Just... where am I going...?" Just then he heard a faint voice talk to him. "I... hear something... were those... voices?"

The voice became clearer as it spoke to him, "Your friend is heartbroken... A true friend... A friend for life..."

Cyndaquil immediately recognized the voice. "That voice... Gardevoir?"

Gardevoir's voice replied, "Yes Cyndaquil. It is me."

Cyndaquil responded, "Why are you communicating with me...?"

Gardevoir explained, "Because you finally realize it now... Chikorita needs you... and you want to stay by her side forever yes?"

"Yes... I want to stay with her, I want to be by her side... I'd give anything for that." Cyndaquil replied earnestly.

Gardevoir replied, "Do you both feel strongly for each other? If your bonds are strong enough to breech time and space... if your bond and wishes burns the stronger... perhaps you will meet again..."

Cyndaquil thought for a moment, "..."

Gardevoir questioned, "Who do you see Chikorita as?"

Cyndaquil remembered all the promises and her face and why he trusted her, and was always close to her... he can no longer deny it... he replied to Gardevoir.

"I don't want to leave... I want to stay by Chikorita's side... always... and it's not by some promise I made to her... it's because... she's my best and an irreplaceable friend... I... I love her."

Gardevoir replied, "Your heart has been tested... Chikorita feels the same... In the universe's time and space... both your bonds, spirits, and loves burn the stronger."

Cyndaquil replied, "Gardevoir... thank you."

Gardevoir responded, "You're welcome. You shall see each other once again!" From somewhere, she used her power and made the light Cyndaquil was encased in, start descending back to the Pokemon World.

 **Scene Shift  
*Song Stop***

The group just returned from their journey back down to Cyndaquil and Chikorita's... well now just Chikorita's team base. It was really late and night time at the moment. Chikorita stared at the entrance that allowed her to see inside, hoping that Cyndaquil was inside, but even she was not that naive.

Chikorita sighed sadly, but didn't cry, "I'm not that naive... I know he's not in there. I will not let Cyndaquil's efforts be in vain... I promised him that I will continue to live my life with no tears."

Caterpie spoke up from behind, "Cyndaquil, he really does mean a lot to you does he?"

The Grass Type, turned red at that but confidently answered, "Yes... he does."

Everyone gave concerned looks toward the young Leaf Pokemon, but then they heard a sound behind them and they all turned around.

"Huh?" Chikorita wondered. They all then saw a burst a of light for a split second, surprising all of them, but Chikorita had a twinkle in her eye. "Oh, c-could it be?"

The light started to glow brighter until with a large glow, Cyndaquil appeared after it faded. Everyone gasped, but Chikorita.

The Grass Type stepped forward, "C-Cyndaquil? Is that really you?"

The Fire Type smiled and nodded, "Yes Chikorita, it really is me."

 ***Song: Staff Credits - Super Mario Galaxy 1 or 2***

The Fire Mouse's partner's eyes gleamed, "Cyndaquil! You're back!" She ran up to him and leaped at him in pure joy and happiness.

Cyndaquil caught her by the stubs and they spun around together, both laughing in relief, joy, and excitement before the hugged and then looked at each other. Cyndaquil told her, "I told you, I'd keep my promise. I'd never leave you."

"YEEEEEEEEEEEEEAAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHHHHHHHHH!" All of the Pokemon were cheering and joyous at their hero and friend's return.

Chikorita asked him, "B-but how did you manage to return to us?"

Cyndaquil took a deep breath and replied, "Gardevoir guided me back, our bonds were strong enough to let me stay."

Chikorita smiled, "Yes, our bonds are strong."

Cyndaquil smiled back, "Our bonds together are strong I know and will keep strengthening because... I love you Chikorita." This caused everyone to be in awe as they bared witness to a human loving a Pokemon, but Chikorita smiled widely and her eyes were twinkling bright.

"Y-you said you loved me." Chikorita said. Cyndaquil just gave a smiling nod.

"Oh Cyndaquil! I love you too!" Chikorita confessed which also shocked team A.C.T, Blastoise and the residents of Pokemon Square that were with them.

They both blushed, but was not embarrassed, this is what they've always dreamed for, they were friends for so long and it's only after the whole ordeal they finally tell each other how they both felt.

"Will we be together forever?" Chikorita asked.

"Together forever." Cyndaquil answered.

They two young Pokemon leaned their faces toward each other and closed their eyes. They pressed their lips together and kissed, both Johto starters savoring the moment, not wanting it to end.

Everyone cheered loudly at the Fire and Grass Type's reunion and gave congratulations for their confession and their advancement in relationship.

The two seperated after a few seconds more and they just stared at each other with warm smiles. They then turned to everyone with a determined and joyous looks.

"Alright everyone! We have a long day ahead of us starting tomorrow!"Chikorita rallied.

"We shall make this world become a better place to be for the happiness and well-fare of everyone living here!" Cyndaquil followed-up.

Cyndaquil and Chikorita cried out in unison, "Let's work together to make this world a place we can be proud of again! Let's give it our all!"

"YYYYYYYYEEEEEEEEEAAAAAAAAAAAAAAAAAHHHHHHHHHHHHH!" All the Pokemon cheered back.

Everyone at the team base partied the whole night away, but Cyndaquil and Chikorita looked at the stars above and said their appreciation together.

"Gardevoir... where ever you are, thank you for uniting us once more." As the two held each other's hands.

* * *

 **Justin: I hope you liked the story! And again my apologies for being absent for 6 months, I was really busy, but rest assured my account is not at all dead! There will be more stories in this series and my other stories too!**

 **Anyway, as per usual please comment and review, I want your thoughts and maybe constructive criticism. But please don't flame, you only lose out in the end.**

 **ANYWAY, THANK YOU SO MUCH FOR READING THIS AND MERRY CHRISTMAS AND HAPPY NEW YEAR! AND REMEMBER, ALWAYS STAY FROSTY! :D**


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